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Cookiecutter specifications


Unique identifier OMICS_09649
Name Cookiecutter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Cookiecutter takes as input one or several FASTQ files or one or several pairs of FASTQ files and requires a file with a list of k-mers for filtering.
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Make, gcc, Python
Maintained Yes


No version available



  • person_outline Aleksey Komissarov

Publication for Cookiecutter

Cookiecutter citations


Clustergrammer, a web based heatmap visualization and analysis tool for high dimensional biological data

Sci Data
PMCID: 5634325
PMID: 28994825
DOI: 10.1038/sdata.2017.151

[…] tive visualizations within shareable Jupyter Notebooks. The Clustergrammer-Widget utilizes the core Clustergrammer-JS and Clustergrammer-PY libraries. Clustergrammer-Widget was built using the widget-Cookiecutter template ( Clustergrammer-Widget can be installed using pip ( and the source cod […]


Extensive unusual lesions on a large number of immersed human victims found to be from cookiecutter sharks (Isistius spp.): an examination of the Yemenia plane crash

PMCID: 5306341
PMID: 27623973
DOI: 10.1007/s00414-016-1449-6

[…] articularly distinctive mouth arranged in a transverse line with hook-like upper teeth and razor-like lower teeth surrounded by fleshy lips (Fig. , ) []. Sucker-like lips and a modified pharynx allow cookiecutter sharks to attach to prey before the lower teeth penetrate the skin (Fig. ) and excise a ‘cookie’ of flesh within seconds (hence the nickname ‘cookiecutter’), then the upper teeth finally […]


Slingshot feeding of the goblin shark Mitsukurina owstoni (Pisces: Lamniformes: Mitsukurinidae)

Sci Rep
PMCID: 4901258
PMID: 27282933
DOI: 10.1038/srep27786

[…] observed in the great white shark Carcharodon carcharias, lemon shark Negaprion brevirostris, sandtiger shark Carcharias taurus, blacktip shark Carcharhinus limbatus, spiny dogfish Squalus acanthias, cookiecutter shark Isistius brasiliensis, and viper dogfish Trigonognathus kabeyai. Therefore, the goblin shark is also unique in the direction of its jaw protrusion.The present in situ video footages […]


The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

Sci Rep
PMCID: 4835728
PMID: 27089831
DOI: 10.1038/srep24501

[…] ses using “Trim Galore!” software ( with default parameters. We then cleaned out reads containing 23-mer Illumina-specific primers using Cookiecutter ( cleaned reads from the microdissected chromosomes were mapped to the three assembled Asian arowana genomes (golden, red and green) us […]


Pathological findings and probable causes of the death of Stejneger’s beaked whales (Mesoplodon stejnegeri) stranded in Japan from 1999 and 2011

PMCID: 4349536
PMID: 25328004
DOI: 10.1292/jvms.13-0454

[…] in Japan [], most previous publications have concerned basic biological data, such as reproductive function, physical maturity and so on (e. g., [, ]). Considering the difference in the frequency of cookiecutter shark bites and Pennella copepod infestation, Stejneger’s beaked whales in the seas around Japan are independent from the population of the same species found along the North American coa […]


Extinction risk and conservation of the world’s sharks and rays

PMCID: 3897121
PMID: 24448405
DOI: 10.7554/eLife.00590.027

[…] ened (n = 16) or Near Threatened (n = 10). Only four are of Least Concern (Salmon shark Lamna ditropis, Goblin shark Mitsukurina owstoni, Longnose pygmy Shark Heteroscymnoides marleyi, and Largetooth cookiecutter shark Isistius plutodus) (). The Indo-Pacific Biodiversity Triangle, particularly the Gulf of Thailand, and the islands of Sumatra, Java, Borneo, and Sulawesi, is a hotspot of greatest re […]


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Cookiecutter institution(s)
Bioinformatics Institute, St. Petersburg, Russia; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Oceanographic Center, Nova Southeastern University Ft Lauderdale, Ft Lauderdale, FL, USA

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